Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Digestive tract
Cell type
DLD-1
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Colon carcinoma
cell line
DLD1
chip antibody
Bethyl Laboratories (A300-055A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was isolated from cells using RNeasy Mini kit (QIAGEN, #74104) and was treated with DNase I(QIAGEN #79254). Immunoprecipitated DNA purified using QIAquik PCR purification kit (QIAGEN, #28106). RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer's instructions. ChIP-seq libraries were prepared from 10 ng of ChIP DNA using the TruSeq ChIP Library Preparation Kit, according to the manufacturer's instructions. Sample preparation for ribosome profiling was conducted according to the manufacturer's specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
33263287
Reads aligned (%)
97.6
Duplicates removed (%)
35.3
Number of peaks
603 (qval < 1E-05)

hg19

Number of total reads
33263287
Reads aligned (%)
97.0
Duplicates removed (%)
36.3
Number of peaks
712 (qval < 1E-05)

Base call quality data from DBCLS SRA